thanks to the authors of the
TRANSCRIPT
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Thanks to the authors of the
Supercomputing 2012 Tutorial,
nominally:
Kenneth Moreland W. Alan Scott Nathan Fabian
Sandia National Laboratories
Utkarsh Ayachit Robert Maynard
Kitware, Inc.
Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company,
under contract DE-AC04-94AL85000.
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Introduction to ParaView
Seán Óg Delaney,
Irish Centre for High End Computing
Visualisation Training Day @ EPCC
Prace Summer of HPC, July 2013
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Outline
ParaView What is it? Why use it? Who uses it?
GUI intro, Graphics Pipeline, File Formats
Filters
Views and Multi-View
Streamlines, Line Plots
Time Dependent Data
Selections
Python traces
Advanced Topics Paraview at scale
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Install ParaView 3.98.1 (or 4.0.0).
http://www.paraview.org Download
Get example material. http://www.paraview.org/Wiki/The_ParaView_Tutorial
Data also available on tutorial handout USB stick.
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Help / Information
Online Help F1
http://paraview.org/Wiki/ParaView/Users_Guide/Table_Of_Contents
The ParaView web page
www.paraview.org
ParaView mailing list
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Why ParaView?
Open-source
Multi-platform
Easy (open, flexible, and intuitive UI).
Scalable (does large visualisations on clusters)
An extensible, modular architecture based on open standards.
A flexible BSD 3 Clause license
Commercial maintenance and support.
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Renato N. Elias, NACAD/COPPE/UFRJ, Rio de Janerio, Brazil Swiss National Supercomputing Centre
Jerry Clarke, US Army Research Laboratory
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Current ParaView Usage
Used by academic, government, and commercial institutions worldwide.
Downloaded ~100K times per year.
HPCwire HPCwire Choice 2010 Awards for Best Visualization Product or Technology.
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ParaView Application Architecture
MPI OpenGL IceT Etc.
VTK
ParaView Server
ParaView Client pvpython Custom App
UI (Qt Widgets, Python Wrappings)
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Data Types
Uniform Rectilinear
(vtkImageData)
Non-Uniform Rectilinear
(vtkRectilinearData)
Curvilinear
(vtkStructuredData)
Polygonal
(vtkPolyData)
Unstructured Grid
(vtkUnstructuredGrid)
Multi-block Hierarchical Adaptive
Mesh Refinement
(AMR)
Hierarchical Uniform
AMR
Octree
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Graphical User Interface (GUI)
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User Interface
Menu Bar
Toolbars
Pipeline Browser
Properties Panel
3D View
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Getting Back GUI Components
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Creating a Cylinder Source
1. menu and select Cylinder.
2. Click the Apply button to accept the default parameters.
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Simple Camera Manipulation
Drag left, middle, right rotate, pan, zoom.
Also use Shift, Ctrl, Alt modifiers.
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Creating a Cylinder Source
1. Go to the Sources menu and select Cylinder.
2. Click the Apply button to accept the default parameters.
3. Change the Height parameter to 0.1.
4. Click the Apply button again.
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Creating a Cylinder Source
5. Look / Scroll down to the Display properties.
6. Click the Edit button under Color.
7. Change the color.
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Creating a Cylinder Source
8. Click on the button at the top of the properties panel.
9. Increase the Resolution parameter.
10. Click the Apply button again.
11. Click again to hide advanced properties.
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Pipeline Object Controls
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Undo Redo
Redo Undo
Camera
Redo
Camera
Undo
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Render View Options
Alternatively, go to Edit -> View Settings...
@ top of layout window
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Display Properties
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Supported Formats (USE ONE!) ParaView Data (.pvd)
VTK (.vtp, .vtu, .vti, .vts, .vtr)
VTK Legacy (.vtk)
VTK Multi Block (.vtm,.vtmb,.vtmg,.vthd,.vthb)
Partitioned VTK (.pvtu, .pvti, .pvts, .pvtr)
ADAPT (.nc, .cdf, .elev, .ncd)
ANALYZE (.img, .hdr)
ANSYS (.inp)
AVS UCD (.inp)
BOV (.bov)
BYU (.g)
CAM NetCDF (.nc, .ncdf)
CCSM MTSD (.nc, .cdf, .elev, .ncd)
CCSM STSD (.nc, .cdf, .elev, .ncd)
CEAucd (.ucd, .inp)
CMAT (.cmat)
CML (.cml)
CTRL (.ctrl)
Chombo (.hdf5, .h5)
Claw (.claw)
Comma Separated Values (.csv)
Cosmology Files (.cosmo, .gadget2)
Curve2D (.curve, .ultra, .ult, .u)
DDCMD (.ddcmd)
Digital Elevation Map (.dem)
Dyna3D(.dyn)
EnSight (.case, .sos)
Enzo boundary and hierarchy
ExodusII (.g, .e, .exe, .ex2, .ex2v.., etc)
ExtrudedVol (.exvol)
FVCOM (MTMD, MTSD, Particle, STSD)
Facet Polygonal Data
Flash multiblock files
Fluent Case Files (.cas)
GGCM (.3df, .mer)
GTC (.h5)
GULP (.trg)
Gadget (.gadget)
Gaussian Cube File (.cube)
JPEG Image (.jpg, .jpeg)
LAMPPS Dump (.dump)
LAMPPS Structure Files
LODI (.nc, .cdf, .elev, .ncd)
LODI Particle (.nc, .cdf, .elev, .ncd)
LS-DYNA (.k, .lsdyna, .d3plot, d3plot)
M3DCl (.h5)
MFIX Unstructred Grid (.RES)
MM5 (.mm5)
MPAS NetCDF (.nc, .ncdf)
Meta Image (.mhd, .mha)
Miranda (.mir, .raw)
Multilevel 3d Plasma (.m3d, .h5)
NASTRAN (.nas, .f06)
Nek5000 Files
Nrrd Raw Image (.nrrd, .nhdr)
OpenFOAM Files (.foam)
PATRAN (.neu)
PFLOTRAN (.h5)
PLOT2D (.p2d)
PLOT3D (.xyz, .q, .x, .vp3d)
PLY Polygonal File Format
PNG Image Files
POP Ocean Files
ParaDIS Files
Phasta Files (.pht)
Pixie Files (.h5)
ProSTAR (.cel, .vrt)
Protein Data Bank (.pdb, .ent, .pdb)
Raw Image Files
Raw NRRD image files (.nrrd)
SAMRAI (.samrai)
SAR (.SAR, .sar)
SAS (.sasgeom, .sas, .sasdata)
SESAME Tables
SLAC netCDF mesh and mode data
SLAC netCDF particle data
Silo (.silo, .pdb)
Spheral (.spheral, .sv)
SpyPlot CTH
SpyPlot (.case)
SpyPlot History (.hscth)
Stereo Lithography (.stl)
TFT Files
TIFF Image Files
TSurf Files
Tecplot ASCII (.tec, .tp)
Tecplot Binary (.plt)
Tetrad (.hdf5, .h5)
UNIC (.h5)
VASP CHGCA (.CHG)
VASP OUT (.OUT)
VASP POSTCAR (.POS)
VPIC (.vpc)
VRML (.wrl)
Velodyne (.vld, .rst)
VizSchema (.h5, .vsh5)
Wavefront Polygonal Data (.obj)
WindBlade (.wind)
XDMF and hdf5 (.xmf, .xdmf)
XMol Molecule
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Load disk_out_ref.ex2
1. Open the file disk_out_ref.ex2.
2. Load all data variables.
3. Click
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Data Representation
Toggle Color
Legend
Mapped
Variable
Representation
Vector
Component
Edit
Colors
Reset Scalar
Range
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Geometry Representations
Points Wireframe Surface Surface
with Edges
Volume
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Introduction to Filters
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Common Filters
Calculator
Contour
Clip
Slice
Threshold
Extract Subset
Glyph
Stream Tracer
Warp (vector)
Group Datasets
Extract Level
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Filters Menu
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Quick Launch
Used for searching for filters by name
Keyboard shortcut
Ctrl-space for Windows & Linux
Alt-space for Mac
Alternatively, go to Filters -> Search...
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Apply a Filter
1. Make sure that disk_out_ref.ex2 is selected in the pipeline browser.
2. Select the contour filter.
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Apply a Filter
3. Change parameters to create an isosurface at Temp = 400K.
Change to Temp
Change to 400
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Apply a Filter
1. Make sure that disk_out_ref.ex2 is selected in the pipeline browser.
2. Select the contour filter.
3. Change parameters to create an isosurface at Temp = 400K.
4.
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Create a Cutaway Surface
1. Select disk_out_ref.ex2 in the pipeline browser.
2. From the quick launch, select Extract Surface.
3.
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Create a Cutaway Surface
1. Select disk_out_ref.ex2 in the pipeline browser.
2. From the quick launch, select Extract Surface.
3.
4. Create a clip filter.
5. Uncheck Show Plane.
6.
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Pipeline Browser Structure Disk_out_ref.ex2
Contour1 DataSetSurfaceFilter1
Clip1
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Reset ParaView
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Views and Multiview
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Multiview
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Multiview
1. Open disk_out_ref.ex2. Load all variables.
2. Add clip filter.
3. Uncheck Show Plane.
4.
5. Color surface by Pres.
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Multiview
1. Split the view horizontally.
2. Make Clip1 visible.
3. Color surface by Temp.
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Multiview
1. Split the view horizontally.
2. Make Clip1 visible.
3. Color surface by Temp.
4. Right-
5. Click other view.
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Multiview
1. Split the view horizontally.
2. Make Clip1 visible.
3. Color surface by Temp.
4. Right-
5. Click other view.
6. Click
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Modifying Views
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Modifying Views
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Reset ParaView
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Streamlines
1. Open disk_out_ref.ex2. Load all variables.
2. Add stream tracer.
3.
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Streamlines
1. Open disk_out_ref.ex2. Load all variables.
2. Add stream tracer.
3.
4. From the quick launch, select Tube
5.
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Getting Fancy
1. Select StreamTracer1.
2. Add glyph filter.
3. Change Vectors to V.
4. Change Glyph Type to Cone.
5.
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Getting Answers
Where is the air moving the fastest? Near the disk or away from it? At the center of the disk or near its edges?
Which way is the plate spinning?
At the surface of the disk, is air moving toward the center or away from it?
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Reset ParaView
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Plotting
1. Open disk_out_ref.ex2. Load all variables.
2. Clip, uncheck, ,
3. Select disk_out_ref.ex2
4. Filters Data Analysis Plot Over Line.
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3D Widgets
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Plotting
1. Open disk_out_ref.ex2. Load all variables.
2. Clip, uncheck, ,
3. Select disk_out_ref.ex2
4. Filters Data Analysis Plot Over Line.
5. Once line satisfactorily located,
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Interacting with Plots
Left, middle, right buttons to pan, zoom.
Mouse wheel to zoom.
Reset view to plot ranges.
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Plots are Views Move them like Views.
Save screenshots.
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Adjusting Plots
1. In Display tab, turn off all variables except Temp and Pres.
2. Select Pres in the Display tab.
3. Change Chart Axis to Bottom Right.
4. Verify the relationship between temperature and pressure.
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Reset ParaView
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Loading Data with Time
1. Open the file can.ex2.
2. Select all variables.
3.
4.
5.
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Animation Toolbar
First
Frame
Previous
Frame Play
Next
Frame
Last
Frame
Loop
Animation
Current
Time
Current
Time Step
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Data Range Workarounds
Open color scale editor dialog
Rescale to Temporal Range
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Save Screenshot/Animation
1. Choose File
2. Complete the subsequent dialogs to save an image.
3. Chose File
4. Complete the subsequent dialogs to save a movie.
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Query-Based Selection
1. Open can.ex2. All variables.
2. Go to last time step.
3. Edit Find Data.
4. Top combo box: find Cells.
5. Next row: EQPS, is >=, and 1.5.
6. Click Run Selection Query.
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Query-Based Selection
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Brush Selection
Surface Cell Selection (shortcut: s)
Surface Point Selection
Through Cell Selection
Through Point Selection
Block Selection (shortcut: b)
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Selection Inspector
Create new selection
Active selection
properties
Selected cells ids
Selection type
Selection display
Properties/Labeling
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Spreadsheet View
1. Split the view
2. In new view, click Spreadsheet View.
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Spreadsheet View
Show only
selected items
Select block
to inspect
What is
shown in
the view
Attribute shown
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Plot Selection Over Time
1. Select a single cell where something
2. From the quick launch, select Plot Selection Over Time
3.
4. In Display panel, select different blocks to plot.
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Reset ParaView
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Extracting a Selection
1. Open can.ex2. Load all variables.
2. Turn off cell labels.
3. Perform a sizeable selection.
4. From the quick launch, select Extract Selection
5.
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Python Trace Demo
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Visualizing Large Models
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Standalone
Client
Data
Server
Render
Server
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Client-Server
Client Data
Server
Render
Server
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Client-Render Server-Data Server
Client Data
Server
Render
Server
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Requirements for Installing ParaView Server
C++
CMake (www.cmake.org)
MPI
OpenGL (or Mesa3D www.mesa3d.org)
Qt 4.6 (optional)
Python (optional) http://www.paraview.org/Wiki/Setting_up_a_ParaView_Server#Compiling
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Connecting to a ParaView Server
http://www.paraview.org/Wiki/Setting_up_a_ParaView_Server#Running_the_Server
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Data Parallel Pipelines Ghost cells can solve most of these problems.
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Data Partitioning
Partitions should be load balanced and spatially coherent.
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Load Balancing/Ghost Cells
Automatic for Structured Meshes.
Partitioning/ghost cells for unstructured is
Use the D3 filter for unstructured
(Filters Alphabetical D3)
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Job Size Rules of Thumb
Structured Data
Try for max 20 M cell/processor.
Shoot for 5 10 M cell/processor.
Unstructured Data
Try for max 1 M cell/processor.
Shoot for 250 500 K cell/processor.
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Avoiding Data Explosion
Pipeline may cause data to be copied, created, converted.
This advice only for dealing with very large amounts of data.
Remaining available memory is low.
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Topology Changing, No Reduction
Append Datasets
Append Geometry
Clean
Clean to Grid
Connectivity
D3
Delaunay 2D/3D
Extract Edges
Linear Extrusion
Loop Subdivision
Reflect
Rotational Extrusion
Shrink
Smooth
Subdivide
Tessellate
Tetrahedralize
Triangle Strips
Triangulate
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Topology Changing, Moderate Reduction
Clip
Decimate
Extract Cells by Region
Extract Selection
Quadric Clustering
Threshold
Similar: Extract Subset
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Topology Changing, Dimension Reduction
Cell Centers
Contour
Extract CTH Fragments
Extract CTH Parts
Extract Surface
Feature Edges
Mask Points
Outline (curvilinear)
Slice
Stream Tracer
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Adds Field Data
Block Scalars
Calculator
Cell Data to Point Data
Compute Derivatives
Curvature
Elevation
Generate Ids
Gen. Surface Normals
Gradient
Level Scalars
Median
Mesh Quality
Octree Depth Limit
Octree Depth Scalars
Point Data to Cell Data
Process Id Scalars
Random Vectors
Resample with dataset
Surface Flow
Surface Vectors
Transform
Warp (scalar)
Warp (vector)
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Total Shallow Copy or Output Independent of Input
Annotate Time
Append Attributes
Extract Block
Extract Datasets
Extract Level
Glyph
Group Datasets
Histogram
Integrate Variables
Normal Glyphs
Outline
Outline Corners
Plot Global Variables Over Time
Plot Over Line
Plot Selection Over Time
Probe Location
Temporal Shift Scale
Temporal Snap-to-Time-Steps
Temporal Statistics
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Culling Data
Reduce dimensionality early.
Prefer data reduction over extraction.
Slice instead of Clip.
Contour instead of Threshold.
Only extract when reducing an order of magnitude or more.
Can still run into trouble.
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Culling Data
Experiment with subsampled data.
Extract Subset
Use caution.
Subsampled data may be lacking.
Use full data to draw final conclusions.
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Rendering Modes
Still Render
Full detail render.
Interactive Render
Sacrifices detail for speed.
Provides quick rendering rate.
Used when interacting with 3D view.
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Level of Detail (LOD) Geometric decimation
Used only with Interactive Render
Original Data Divisions: 50x50x50 Divisions: 10x10x10
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3D Rendering Parameters Edit Settings, Render View General
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Image Size LOD
proportional to image size.
Can use smaller images for interactive rendering.
Original Data Subsample Rate: 2 pixels Subsample Rate: 4 pixels Subsample Rate: 8 pixels
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Parallel Rendering Parameters Edit Settings, Render View Server
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Parameters for Large Data
Use Immediate Mode Rendering off for GPU, on for CPU.
Try LOD Threshold off.
Also try LOD Resolution 10x10x10.
Always have remote rendering on.
Turn on subsampling.
Image Compression on.
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Parameters for Low Bandwidth
Try larger subsampling rates.
Try Zlib compression and fewer bits.
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Parameters for High Latency
Turn up Remote Render Threshold.
Turn on Use outline for LOD rendering if necessary.
Play with the LOD Threshold and LOD Resolution to control geometry sent to client.
Try turning on Lock Interactive Render.
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Further Reading
Amy Henderson Squillacote. The ParaView Guide. Kitware, Inc., 2006.
http://www.paraview.org/Wiki/ParaView
http://www.paraview.org/Wiki/Setting_up_a_ParaView_Server